Literature DB >> 24767259

Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.

Liang Xu1, Linati Da1, Steven W Plouffe1, Jenny Chong1, Eric Kool2, Dong Wang3.   

Abstract

Maintaining high transcriptional fidelity is essential for life. Some DNA lesions lead to significant changes in transcriptional fidelity. In this review, we will summarize recent progress towards understanding the molecular basis of RNA polymerase II (Pol II) transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis. In particular, we will focus on the three key checkpoint steps of controlling Pol II transcriptional fidelity: insertion (specific nucleotide selection and incorporation), extension (differentiation of RNA transcript extension of a matched over mismatched 3'-RNA terminus), and proofreading (preferential removal of misincorporated nucleotides from the 3'-RNA end). We will also discuss some novel insights into the molecular basis and chemical perspectives of controlling Pol II transcriptional fidelity through structural, computational, and chemical biology approaches.
Copyright © 2014 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Chemical biology; Computational biology; DNA damage recognition; Fidelity control; Nonpolar isostere; RNA polymerase II; Structural biology; Synthetic nucleotide analogs; Transcription elongation; Transcriptional lesion bypass; Unlocked nucleic acid

Mesh:

Substances:

Year:  2014        PMID: 24767259      PMCID: PMC4051827          DOI: 10.1016/j.dnarep.2014.03.024

Source DB:  PubMed          Journal:  DNA Repair (Amst)        ISSN: 1568-7856


  169 in total

1.  Transcription elongation factor S-II maintains transcriptional fidelity and confers oxidative stress resistance.

Authors:  Hiroshi Koyama; Takahiro Ito; Toshiyuki Nakanishi; Nobuyuki Kawamura; Kazuhisa Sekimizu
Journal:  Genes Cells       Date:  2003-10       Impact factor: 1.891

2.  Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes.

Authors:  Rodney G Weilbaecher; Donald E Awrey; Aled M Edwards; Caroline M Kane
Journal:  J Biol Chem       Date:  2003-04-11       Impact factor: 5.157

3.  Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.

Authors:  Jasmin F Sydow; Florian Brueckner; Alan C M Cheung; Gerke E Damsma; Stefan Dengl; Elisabeth Lehmann; Dmitry Vassylyev; Patrick Cramer
Journal:  Mol Cell       Date:  2009-06-26       Impact factor: 17.970

4.  RNA polymerase II transcript elongation.

Authors:  Jesper Q Svejstrup
Journal:  Biochim Biophys Acta       Date:  2013-01

5.  RNA polymerase II blockage by cisplatin-damaged DNA. Stability and polyubiquitylation of stalled polymerase.

Authors:  Yongwon Jung; Stephen J Lippard
Journal:  J Biol Chem       Date:  2005-11-07       Impact factor: 5.157

6.  The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.

Authors:  M D Rudd; M G Izban; D S Luse
Journal:  Proc Natl Acad Sci U S A       Date:  1994-08-16       Impact factor: 11.205

7.  Yeast transcript elongation factor (TFIIS), structure and function. II: RNA polymerase binding, transcript cleavage, and read-through.

Authors:  D E Awrey; N Shimasaki; C Koth; R Weilbaecher; V Olmsted; S Kazanis; X Shan; J Arellano; C H Arrowsmith; C M Kane; A M Edwards
Journal:  J Biol Chem       Date:  1998-08-28       Impact factor: 5.157

8.  Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase.

Authors:  Vasily Sosunov; Ekaterina Sosunova; Arkady Mustaev; Irina Bass; Vadim Nikiforov; Alex Goldfarb
Journal:  EMBO J       Date:  2003-05-01       Impact factor: 11.598

Review 9.  Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects.

Authors:  Maria Fousteri; Leon H F Mullenders
Journal:  Cell Res       Date:  2008-01       Impact factor: 25.617

10.  Active site opening and closure control translocation of multisubunit RNA polymerase.

Authors:  Anssi M Malinen; Matti Turtola; Marimuthu Parthiban; Lioudmila Vainonen; Mark S Johnson; Georgiy A Belogurov
Journal:  Nucleic Acids Res       Date:  2012-05-08       Impact factor: 16.971

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  19 in total

1.  Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.

Authors:  Liang Xu; Wei Wang; Jiabin Wu; Ji Hyun Shin; Pengcheng Wang; Ilona Christy Unarta; Jenny Chong; Yinsheng Wang; Dong Wang
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-07       Impact factor: 11.205

2.  RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications.

Authors:  Ji Hyun Shin; Liang Xu; Dong Wang
Journal:  Transcription       Date:  2016-04-22

Review 3.  Mechanistic insights into transcription coupled DNA repair.

Authors:  Bibhusita Pani; Evgeny Nudler
Journal:  DNA Repair (Amst)       Date:  2017-06-09

Review 4.  RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.

Authors:  Liang Xu; Wei Wang; Jenny Chong; Ji Hyun Shin; Jun Xu; Dong Wang
Journal:  Crit Rev Biochem Mol Biol       Date:  2015-09-22       Impact factor: 8.250

5.  Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase.

Authors:  Aleksei Agapov; Daria Esyunina; Andrey Kulbachinskiy
Journal:  RNA Biol       Date:  2019-08-21       Impact factor: 4.652

6.  Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1.

Authors:  Catherine Schalk; Valérie Cognat; Stéfanie Graindorge; Timothée Vincent; Olivier Voinnet; Jean Molinier
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-21       Impact factor: 11.205

Review 7.  Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest.

Authors:  Juntaek Oh; Jun Xu; Jenny Chong; Dong Wang
Journal:  Methods       Date:  2019-02-22       Impact factor: 3.608

Review 8.  Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair.

Authors:  Wei Wang; Jun Xu; Jenny Chong; Dong Wang
Journal:  DNA Repair (Amst)       Date:  2018-08-23

9.  The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro.

Authors:  Marina Kolbanovskiy; Moinuddin A Chowdhury; Aditi Nadkarni; Suse Broyde; Nicholas E Geacintov; David A Scicchitano; Vladimir Shafirovich
Journal:  Biochemistry       Date:  2017-06-07       Impact factor: 3.162

10.  Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

Authors:  Candy S Hwang; Liang Xu; Wei Wang; Sébastien Ulrich; Lu Zhang; Jenny Chong; Ji Hyun Shin; Xuhui Huang; Eric T Kool; Charles E McKenna; Dong Wang
Journal:  Nucleic Acids Res       Date:  2016-04-07       Impact factor: 16.971

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